For an everyday player the standard 5 game suspension for misconduct certainly hurts both the player and the team as a whole. Whereas, the same standard 5 game suspension for pitcher doesn't even result in a pitcher missing a start (next game).

Why are MLB pitchers suspended with the same standard procedures as everyday position players?

2 Answers
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In baseball, any player can play any position (unlike, say, rugby where certain positions can only be played by designated players). This is why it has been possible for a single player to play every single baseball position in a single game. There is nothing stopping a team playing their normal catcher as a pitcher or a starting pitcher in any other position.

I think that MLB suspensions are equal for all players because pitchers are not officially registered as being pitchers. Consequently, the leagues do not enforce that a player always plays in a certain position. Therefore, MLB doesn't have the right to give a longer suspension to a player only because he usually plays as a pitcher (even though everyone knows he actually is a pitcher). The equal suspensions for all players is probably part of the collective bargaining agreement between the leagues and the players' union.

This isn't exactly an accurate question. MLB starting pitchers are generally suspended for 5 games at a minimum, which is intended to mimic being suspended for a start. While it doesn't exactly mean a start is missed, it does affect the team - you need 5 other starters for those 5 games, likely meaning you are starting someone who wouldn't normally start, or someone from AAA, or you're starting someone on short rest.

This is most easily seen in the default suspensions for actions a pitcher would likely take. In recent years (more recent than the question, following the latest CBA largely) starting pitchers are actually given 6 games commonly, which will often reduce their total start count for the season.

In the case of things like brawls, starting pitchers get similar levels to position players, except they usually start at 5 games. That's reasonable, because it's a similar proportion of the season for them (2/32 instead of 10/162, both are effectively 1/16). Ian Kennedy for example received 10 games, or effectively 2 starts, for his role in starting the Dbacks-Dodgers brawl in 2013; only one other player received even 5 games.